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Set in Japan 1000 years after the modern era, Shin Sekai Yori follows the life of Saki Watanabe, a girl from the town of Kamisu 66. In this era, all humans possess powerful psychic abilities and live an idyllic life in agrarian villages. Despite her parents' fears that she may not awaken her powers, Saki gains her special powers at the age of twelve and joins her friends—Satoru Asahina, Maria Akizuki, Mamoru Itou, Shun Aonuma, and Reiko Amano—in Sage Academy, a special school for psychics. However, the children are unaware that the village government is monitoring and evaluating students through the education system. Based on these evaluations, certain students are removed from society because of reasons such as poor performance (such as with Reiko) or for cheating. The memories of the removed students are erased from the community; Saki and her remaining friends have no memory of Reiko and other students. During an unsupervised camping field trip, Saki and her friends capture a False Minoshiro, a mythical animal revealed to be an ancient library robot. The False Minoshiro explains the violent truth of how the current era came about and what their special powers truly are.

In AD 2013, 0.3 percent of the population developed psychic abilities that allowed them to alter their surrounding environment. Soon after the powers manifest, many begin using them for violence and crime. This leads to a breakdown of modern society and a world war that devastates the human population. The conscious and unconscious use of these powers alter the wildlife and the environment. After the fall of modern society, oppressive, feudalistic regimes rise up over humanity. These regimes, too, dissolve in chaos due to the violence of the psychic humans. Eventually, the psychic endowed humans established a stable society where they control their powers by using genetic modification and social conditioning to make themselves incapable of violence against other humans (Attack Inhibition). If a psychic human kills another, a biological Death Feedback is activated, causing the murderer's organs to shut down and the attacker to die almost instantly. The villages also use genetically designed animals for various purposes. The mole-like Monster Rats resemble humanity, able to speak human language and living in a complex eusocial society ruled by queens. The feline Impure Cats are used to kill children at risk of developing one of the two dangerous disorders: the Karmic Demons (業魔,Gōma), who are unable to control their powers, and the Ogres (悪鬼,Akki), who can suppress the Attack Inhibition and Death Feedback and use their special powers against humans.

In the middle of interrogating the False Minoshiro, Saki and her friends are found by the monk Rijin. He destroys the False Minoshiro and seemingly seals away the children's special powers for associating with a demon. On the way back to be judged at the village, Rijin is killed by a rogue Monster Rat tribe while Saki and Satoru are separated from their friends. They are captured by the rogue Monster Rat colony. Using objects found during their trip, Saki and Satoru are able to escape their prison. During their escape, they meet a Monster Rat, Squealer, of the Robber Fly colony who rescues them from their pursuers. Saki and Satoru help Squealer and his colony to defeat the rogue monster rats, later with assistance from General Kiroumaru and his Giant Hornet colony, a colony with an especially close relationship to humans. After regrouping with their friends with the help of Squealer and general Kiroumaru, Saki restores their powers, using the same hypnotic methods the village uses to control children, before returning to the village under the belief that the adults do not know of their transgressions.

Two years later, as Saki and her friends reach adolescence and develop relationships, Shun starts to distance himself from the others and eventually goes missing. Saki finds Shun in an abandoned house and learns that he has become a Karmic Demon and had been sent to die in isolation. After holding himself back for the duration of their meeting, Shun tells Saki to go while telling her the adults know of their transgressions two years ago before using his powers to take his own life. Soon after, unlike with Reiko, Saki and her remaining friends start to realize Shun's absence despite being unable to fully remember him. In time, Saki learns that the survival of herself and her friends has been orchestrated by the Education board and the Ethics Committee Head Tomiko Asahina, who sees Saki as a potential successor. Later, Mamoru and Maria run away after the Education Board tries to purge Mamoru. Squealer, renamed by the humans as Yakomaru as a reward for his usefulness, helps them by staging their deaths. However, after finding the Robber Fly queen lobotomized and that Yakomaru acquired a False Minoshiro, Saki begins to have dreams of a faceless child that tells her not to find Mamoru and Maria as they must die.

Now 26 years old, Saki works for the village government in the "Department of Mutant Management" which oversees the Monster Rats. Yakomaru's colony slowly ascends to power while conquering other colonies and wiping out the Giant Hornet colony, eventually attacking Kamisu 66 with what is believed to be an Ogre that the Monster Rats refer to as their "Messiah." This is later revealed to be the biological child of Mamoru and Maria who Yakomaru raised after murdering the parents. After evading the Ogre and learning that Yakomaru intends to steal more human infants to create an army to wipe out the human race, Saki and Satoru are joined by Kiroumaru who guides them to the ruins of Tokyo to find the "Psychobuster"; an anthrax-like anti-psychic weapon. With Yakomaru's forces surrounding them, Satoru attempts to kill the Messiah with the Psychobuster, but Saki destroys the weapon because its use at such close proximity would also have killed Satoru. Saki realizes that the Messiah is not truly an Ogre, but actually a regular psychic like themselves, with one key difference: the Messiah considers Monster Rats as his kin which is what enables him to bypass the Death Feedback when attacking other humans. With seemingly no options left, Saki and Satoru plead with Kiroumaru for help. After admitting his own disdain towards humans and their treatment of his kind, Kiroumaru agrees to help, but asks for his colony to be spared the humans' retaliation once the revolt is ended. He disguises himself as a human and attacks the Messiah. The Messiah kills Kiroumaru, but upon realizing that Kiroumaru is a Monster Rat, dies due to Death Feedback.

With the Messiah dead and his rebellion crushed Squealer is defeated. Renouncing the name the humans gave him, Squealer is sentenced to perpetual torture of the "Infinite Hell" where his body is simultaneously regenerated and destroyed using psychic powers. However, Saki is troubled when Squealer explains the reasons behind his revolt, claiming that his people are human. Later, Saki learns from Satoru that the Monster Rats are the descendants of normal humans whose DNA had been altered with mole rat genes to make it easier for the psychic humans to control them, since they will not trigger Attack Inhibition and Death Feedback. Now feeling sorry for Squealer, Saki secretly puts him out of his misery.

In the epilogue ten years later, Saki has married Satoru and they expect their first child. Both are positive that the world will be a better place by the time their child grows up.

Initially, Saki is 12 years old, has short brown hair and argues a lot her hair now shoulder-length, she becomes Maria's girlfriend. Despite that, her feelings for Shun remain strong. After several incidents occur, she is eager to know the true secrets of the town. Tomiko also reveals that she has a strong mental stability capable of overcoming setbacks. After the second timeskip, she is 26 and now works at the Department of Mutant Management, investigating and regulating the Monster Rat colonies. In the epilogue, she marries Satoru and succeeds Tomiko as head of the Ethics Committee. Pregnant, Saki writes her experiences down so future generations would read in hope the world becomes a better place.

Satoru is an energetic and mischievous boy who likes to argue with Saki. He is also observant, smart and skillful in using his telekinesis. After the timeskip, Satoru becomes Shun's boyfriend, but he starts dating another boy shortly after their breakup. After a second timeskip, he becomes Saki's partner and closest friend. He is adept at creating reflections, in the form of creating mirrors out of air - a skill that turns out to be incredibly useful. After the battle with the Monster Rats, Satoru also discovers the disturbing truth about the Monster Rats' origin and years later, becomes Saki's husband.

Shun is the smartest and most composed of the group of friends and is able to think his way out of any situation. He is also very knowledgeable. Shun is also implied to be the most talented telekineticist of their generation. After the timeskip, he becomes Satoru's boyfriend, but later breaks up with him. Eventually he loses control of his telekinesis, turning him into a Karmic Demon (業魔,Gōma). It is also revealed that Shun had loved Saki since childhood, but he chose to avoid her due to his growing uncontrollable power. Near the end, he seems to have manifested a part of himself in Saki's consciousness, giving her crucial advice in order to change her decisions in the last few episodes.

Maria has long red hair and is stated to be the most popular girl in her class. After the timeskip, she develops feelings for Saki and becomes her girlfriend, although she later forms a duty pair with Mamoru. She is particularly adept at matter movement (e.g. levitation). After Mamoru runs away, she leaves the others to join him. It is revealed that she was pregnant with Mamoru's child and was held by the Robber Fly colony before she was murdered upon her child's birth.

Mamoru is the most timid and the least talented of the group. Following the timeskip, he grows to have a crush on Maria and eventually partners with her as a duty pair. After learning about the Board of Education's plans to dispose of him, he leaves the village and hides in the mountains. Maria promises him that they will never be apart again, subsequently joining him and leaving the others behind. After the second time skip, with Tomiko confirming it, Mamoru was killed by the Robber Fly Monster Rats and had a child with Maria that Squealer raised to be the Monster Rats' "Messiah".

Satoru's grandmother and also the head of the Ethics Committee. She intends for Saki to succeed her position as she possesses a strong mental stability as well as the qualities of a leader. Because of this, she had asked the Board of Education not to dispose of Saki and her friends despite knowing about the true history. She also revealed that they were responsible for erasing their bad memories of the past to protect the minds of the townsfolk. With the ability to regenerate the telomeres in her cells, Tomiko has managed to extend her life, having lived for more than 250 years. She also had a close encounter with an Ogre (悪鬼,Akki) in the past.

The adviser of the Security Council and also the village's strongest telekineticist. He wears a hooded mask and has double irises in each eye, capable of detecting and dispelling attacks from all directions. He also displays calmness and confidence in retaliation against the Monster Rats' attack on the village but is still powerless against the Ogre.

A Wildlife Protection officer. He was tasked to annihilate the Robber Fly colony and its allies but his mission failed. He was saved by Kiroumaru and he later accompanied Saki's group to Tokyo for her mission.

The Monster Rats (バケネズミ,Bakenezumi) are humanoid molerat mutants who live in colonies and appear obedient to the humans to the point of referring to them as gods. However, during the attack on the humans by Squealer, it's revealed that the Monster Rats disdain humans for the way they're treated. Saki eventually learns to her horror that Monster Rats are actually the descendants of normal humans who were genetically modified with molerat DNA to enable the humans with special powers to subjugate those who don't suffer the Death of Shame, whom they would otherwise be defenseless against.

Starting off as a lowly member of the Robber Fly colony who once offered help to Saki and Satoru, Squealer eventually attains knowledge and gains political clout to become the supreme commander of the Robber Fly colony, earning the name 'Yakomaru' while exhibiting a machiavellian nature. Despite being a weak and small colony initially, the Robber Fly colony grew to rival the Giant Hornets colony after the second timeskip. He initially appears to be faithful to the humans, but secretly learned the truth of his kind's origin, after which he planned to wipe out the human population and liberate all Monster Rats. The opportunity came when he had the runaway Maria and Mamoru murdered to obtain their newborn child to raise as both one of his own and as the Monster Rats' "Messiah". Squealer's plan was thwarted by Saki and he was later sentenced to suffer the 'Infinite Hell', consumed by his own nervous system and in agonizing pain. However, upon learning the truth behind the Monster Rats, Saki secretly gives Squealer a merciful death.

The supreme commander of the Giant Hornet colony, he risked his own life to let Saki and Satoru return to their friends instead of executing them. Much later on, Kiroumaru's colony was decimated by the Robber Fly colony with the aid of their "Messiah" and he ended up at the Temple of Purification. After being released by Saki, Kiroumaru leads her and her group to the ruins of Tokyo to obtain the Psycho Buster to thwart Squealer's plans. After the plan with the Psycho Buster fails, revealing his own disdain for humans, Kiroumaru asks Saki to spare his colony from the humans' retaliation as he sacrifices himself to defeat the "Messiah".

A member of the Goat Moth colony. Saki saved him from drowning when he fell into a river. Two years later, he repaid the favor by saving Mamoru after he fell off a cliff. He gives Saki a letter from Maria.

The novel From the New World was written by the Japanese author Yusuke Kishi and published by Kodansha. Its original publication was on January 23, 2008, in two volumes.[6][7] It is believed that the author has remained "silent" three years prior to publishing the novel. On August 7, 2009, it was re-released as a single volume under the Kodansha Novels imprint[8] and again on January 14, 2011, as three volumes under the Kodansha Bunko imprint.[9][10][11]

A manga adaption of the novel, drawn by Tōru Oikawa, was serialized in Kodansha's Bessatsu Shōnen Magazine. The first chapter was published in the June 2012 issue on May 9, 2012,[12] and the final in the July 2014 issue on June 9, 2014.[13] The series has been collected in seven tankōbon volumes under the Kodansha Comics imprint, released between October 9, 2012,[14] and August 8, 2014.[15] In 2013 the series was licensed in English by Vertical Inc, who released it between November 12, 2013,[16][17] and January 20, 2015.[18]

The novel was adapted into an anime television series by A-1 Pictures which aired on TV Asahi from October 2012 to March 2013.[29][30] It has been licensed by Sentai Filmworks in North America.[31] The anime does not have an opening theme but theme songs that are played during the closing credits. "Wareta Ringo" (割れたリンゴ, lit. Sliced Apple) by Risa Taneda was used for episode 1 through 16, which was replaced by "Yuki ni Saku Hana" (雪に咲く花, lit. The Flower Blooming in Snow) by Kana Hanazawa starting in episode 17.[32]

"The Season of New Leaves"Transcription: "Wakaba no Kisetsu" (Japanese: 若葉の季節)

October 3, 2012 (2012-10-03)

In the year 2011, humans begin to manifest psychokinetic powers, leaving a trail of death and destruction in their wake. 1000 years later, Saki Watanabe finally has her own powers awakened, and after a ritual of passage, she rejoins her friends at school who had awakened before her. However, one of them, Reiko, is revealed to have weaker control over her powers than her peers, and soon afterwards she mysteriously disappears.

Saki and her friends in Group 1 take part together in a game tournament where each group must control small clay dolls with their power. Her team defeats several opponents until the final match when one of the members of the opposing team breaks the rules, ending the match in a draw. After the tournament, the same student is never seen again.

While the members of Group 1 set out for summer camp together, Reiko is easily forgotten. Satoru starts telling scary stories about Balloon Dogs, a creature capable of causing itself to explode; the other children doubt its existence, rationalizing that none would exist if they all blew up. The children recall the legend of a strange creature known as the "False Minoshiro" which brings death to all in its path. Eager to learn more about it, they manage to locate and capture the Minoshiro, which much to their surprise, starts communicating with them.

The children learn from the Minoshiro the truth about the tragic history of the world since the advent of humanity's psychokinetic powers 1000 years ago until they are intercepted by a monk who kills the False Minoshiro, seals their powers, and takes them away to be judged for their actions. Due to killing the False Minoshiro, the monk experiences a phenomenon called the death feedback, which hinders his ability to think properly. On the way, they are attacked by a group of Monster Rats, who are slain by the monk until a Balloon Dog leaps toward them.

5

"Pursuit on a Hot Night"Transcription: "Tōbō no Nettaiya" (Japanese: 逃亡の熱帯夜)

October 31, 2012 (2012-10-31)

The Balloon Dog explodes, killing the monk and itself. Defenseless against the Monster Rats, the children flee, with Saki and her friend Satoru being separated from the others and captured by Monster Rats. After escaping confinement, the pair is rescued by Squealer, a Monster Rat from the "Robber Fly" colony who brings them before his queen and asks for their help against their rivals of the "Ground Spider" colony, who threaten to ravage the Robber Fly settlement. Saki and Satoru do not reveal to them that their powers are sealed, and flee by themselves when the invasion begins.

Saki and Satoru appear to be trapped with no chance to escape. Saki deduces that they were all hypnotized into forgetting their mantras, which are necessary to use their telepathic powers. She uses hypnosis to recover his powers by telling him his mantra, which she had secretly tricked from him in their childhood. Instead of fleeing with her, Satoru decides to fight the Monster Rats of the Ground Spider colony, aided by Squealer and the surviving Robber Fly warriors. As the group survives several enemy ambushes, Satoru begins to show signs of fatigue from overusing his abilities, but despite Saki's protests, he continues on until they encounter a massive army of Monster Rats.

The Giant Hornet colony arrives and annihilates the Ground Spiders. Satoru agrees to accompany the Giant Hornet leader Kiroumaru to the Ground Spiders' nest, where they are attacked by the Ground Spiders' commander. Satoru suspects that Kiroumaru may have received an order to kill him and Saki, and they flee through the forest, guided through a shortcut by Squealer. Upon arriving at the river, they are reunited with their friends. As they are returning to town, they encounter Kiroumaru, who helps them by towing their canoes behind his ship. In parting, he asks that they keep his assistance a secret, suggesting he may have defied orders to kill or capture them. Saki restores Shun's telepathic powers and offers to help the others restore theirs.

Two years pass, and the children enter adolescence. Saki finds her feelings for Shun unrequited when he starts dating Satoru instead and she starts dating Maria. Soon after, Shun breaks up with Satoru and starts distancing himself from everyone else. Saki questions him about the reason and learns from him that the adults know the truth about what happened two years ago. He also warns her to be careful because the time for them to be punished for their past transgressions may come soon.

Shun stops coming to school, and his friends in Group 1 start looking for him in secret. Saki and Satoru set out for Shun's home village of Pinewood, only to find it isolated by the authorities and Shun's house destroyed. Later at night, Saki confronts her parents about what really happened to the village but they have been forbidden to tell her the truth. Soon after, Saki is visited by Maria, who reveals to her she and Mamoru learned that several Impure Cats (不浄猫,fujō neko), used to eliminate troublesome children, are being maintained at the school, and two were freed to hunt down Shun. Saki flees to warn him just to come across one of the Impure Cats.

Protected by a charm she got from Shun, Saki manages to defeat the Impure Cat before meeting him. Shun reveals to her that his entire village was destroyed because his powers went out of control. She also learns from him that the drastic alteration in the world's fauna and flora seen in the last 1000 years was due to the residual energy that flows from humans whose powers are not in full control; the safehouse where he is being kept is bizarrely warped and his pet bulldog Subaru mutated into a monstrous form by the leakage from his powers. Subaru is killed protecting Shun from the other Impure Cat, which has been sent to kill him, and Shun subsequently kills it. With little time left before he is killed by his own uncontrolled power, Shun reveals to Saki that he always loved her before having her flee to safety.

As part of their schooling, each student will be paired with a partner of the opposite sex for further training. Saki's classmate Ryou is interested in partnering with her, but as Saki realizes that he is not who she thought him to be, she turns him down and pairs up with Satoru instead. While talking to their friends, Saki realizes that their memories were altered so they recognize Ryou as a regular member of the group since childhood instead of Shun, whose name they can't manage to remember. Mamoru starts remembering Reiko, who disappeared soon after Saki joined the school, but cannot recall her name either. Saki finds a mirror in an old crate, which when polished reveals the name Yoshimi. This is the name of Saki's older sister, who the children deduce (due to the poor writing on the mirror) had poor control over her powers and was thus eliminated. Mamoru begins to panic, so Saki, Satoru and Maria decide to keep investigating by themselves without him, but soon after they are called for an audience with Satoru's grandmother Tomiko, who is revealed to be the head of the Ethics Committee, a fact that not even Satoru was aware of.

Tomiko reveals to Saki the truth behind Ogres and Karmic Demons, including their reasons for the harsh means they developed to prevent them from appearing, and that she was the one who intervened and had Saki and her friends spared by the Board of Education after the incident with the False Minoshiro. Tomiko tells Saki that she is considered the most suited one to be her successor. Some time later, Mamoru mysteriously runs away from home and Saki, Maria and Satoru take advantage of a break in classes to look for him.

Saki and the others follow Mamoru's tracks until finding him in a shelter. They also meet Squonk, a Monster Rat who Saki saved from drowning years before, who has just saved Mamoru's life. Mamoru reveals to them that he left the village in fear because he has been followed for some time an Impure Cat and was led to the location near the courtyard by his teacher, signs that the Board of Education decided to dispose of him.

Saki and Satoru leave Maria behind with Mamoru in care of the Monster Rats and return to the village. Saki is grilled by the Board of Education but is released after Tomiko again intervenes on her behalf. Tomiko reveals that the members of Group 1 were selected for special treatment since childhood. They have been spared most of the hypnotic conditioning and memory alteration that is routinely used to instill obedience and docility. Tomiko predicts that the Board will order the destruction of both Mamoru and Maria, but says she can delay this for three days. Saki and Satoru head off to try to bring the others back before this deadline.

Saki and Satoru keep searching for Maria and Mamoru until an accident leaves Saki unconscious. She awakens beside Satoru in a cabin at the Robber Fly village, where they are reunited with Squealer, who has now taken the name Yakomaru. As the two are brought before the Monster Rats' queen, they learn from Squealer that the Robber Fly society has greatly advanced since their last meeting, and are now part of a strong confederation of colonies, but the two are shocked when they find that the queen was restrained and lobotomized by her own children. Squealer claims that it was all for the good of the colony, by containing the frenzied queen while preserving her capacity to reproduce. The concrete houses and other technology the colony now employs lead Satoru to believe that the Robber Fly colony has captured a False Minoshiro and accessed the knowledge it holds. Doubting Yakomaru's true intentions, the pair is escorted by him and his soldiers to the nest of the Goat Moth colony, where Squonk lives, to ask him about the whereabouts of their missing friends. After Yakomaru calls to them with no answer, a skirmish begins between the two parties until Satoru uses his power to stop them. Finally reunited with Squonk, Saki receives from him a letter left behind by Maria before she departed with Mamoru to parts unknown.

Saki reads Maria's farewell letter, asking her to tell the villagers that she and Mamoru are dead. Despite Maria's instructions, and with only a day left, Saki and Satoru continue to search for them. As hope dwindles, Saki begins to experience bizarre and troubling nightmares of a faceless boy who tells her not to aid in her friends' escape, and that Maria has to die.

Several years later, Saki, now 26 years old, is working in the "Department of Mutant Management". She is visited at work by Satoru, bringing news of an unprovoked attack among the Monster Rats, whose colonies are now divided into two large alliances. Kiroumaru and Yakomaru, the leaders of the opposing alliances, are summoned to be questioned about the incident, but with both leaders exchanging accusations, no conclusion is reached and some time later, the conflict between both parties escalates into a war. In the first battle, Kiroumaru's Giant Hornet army defeats their opponents, which for some reason did not include members of the main enemy colony, the Robber Flies, led by Yakomaru. Some time later, Saki is visited by Satoru again who informs her that the Giant Hornets were annihilated.

An investigation is conducted regarding the demise of the Giant Hornets, but finds no conclusive evidence of how the Robber Flies were able to defeat their superior opponents with such ease; however, the lack of damage to weapons on the battlefield point to the possibility that a human's telekinesis was used in the battle. The council decides unanimously to wipe out the Robber Fly colony. Shisei Kaburagi, the security council advisor and a powerful monk, suspects that Maria and Mamoru are behind the attack, but Tomiko dismisses this with the revelation that Maria and Mamoru's bones were recovered and DNA testing proved that both of them are dead. This news shocks Saki, who Satoru later comforts. Despite some concerns over the matter with the Monster Rats and one councilmember's desire to postpone it, a planned summer festival is held in the village. On the night of the festival, the Monster Rats stage a surprise attack on the village. Satoru and Saki are caught in the commotion but they are saved by Kaburagi, who uses his great telekinetic powers to drive away the enemy. With many casualties and the village in state of emergency after the attack, Tomiko swears she will make Yakomaru pay dearly for his treason.

In the aftermath of the Monster Rats' sneak attack, Saki and Satoru join up with another group and accompany them to the hospital to check on one of their injured friends. As they arrive, they find the hospital destroyed. After clearing the place of the Monster Rats and rescuing the few survivors, the party is attacked by an unknown individual who kills everyone in its path with an overwhelming power. Fearing that the enemy in question may be an Ogre, the other members of the party decide to sacrifice themselves to let Saki and Satoru to escape and warn the others. However, as they flee along the river, the duo soon realize that they are being followed by the enemy.

Saki and Satoru create a diversion and manage to escape their boat before the Ogre incinerates it. They continue on to the village in order to warn the townspeople, but come across a mutant fish that attacks them, blowing itself up in a suicide attack. Saki is blown away by the explosion and separated from Satoru. While in midair, she has a flashback of her parting with Shun, although still she cannot remember his name or face. When she lands, she is attacked by flying boulders and fears the Ogre has found her until her attacker reveals himself as a young boy, who mistook her for a Monster Rat. They continue to the village, which is now in shambles with many dead or injured. The canals have been drained in order to prevent the mutant fish from accessing the town, but Saki wonders if this was Yakomaru's attempt at cutting off their only means of transportation. She finds an injured Tomiko, who refuses to believe that an Ogre is on the loose. She tells Saki to find the Security Council and warn the others, while she stays behind. Saki protests, but Tomiko formally requests that she take charge of the Ethics Committee, and that it is now her duty to protect the town. Saki departs the hospital, leaving Tomiko behind.

21

"The Fire that Destroys the World"Transcription: "Gōka" (Japanese: 劫火)

February 27, 2013 (2013-02-27)

Saki and Niimi, her coworker, decide to head to the Temple of Purity, as Kaburagi declares war on the Monster Rats, promising to eliminate them from Japan. But the Ogre approaches, killing many humans as it comes to confront Kaburagi. Saki sees the Ogre and is shocked by its resemblance to Maria. Satoru appears and tells Saki and Niimi that they have to leave as soon as possible, since even Kaburagi cannot kill an Ogre. Though Kaburagi manages to evade the Ogre's first attack, she kills him. Saki and the others run, confronting a Monster Rat along the way who tells them that the Monster Rat race will now be the new rulers, and that their "Messiah", the Ogre, was sent from the heavens to save them. They kill the Rat, and Niimi tells them he must leave them and go to the Town Hall. Saki and Satoru make it to the Temple of Purity, where they learn that Saki's parents have already been there and plan to release the remaining Impure Cats upon the Ogre. They also meet up with Inui, who tells them about his group's failed mission to dispose of the Robber Fly colony and his first encounter with the Ogre. When he made it back to the village alone following his group's death, he found the hospital burned down and all the human infants stolen. It is then that Saki realizes that Yakomaru killed Maria and Mamoru, took their child, and raised it to become an Ogre. He plans to do the same with the stolen infants, creating an army of Ogres that will wipe the humans off the face of the Earth and bring rise to a Monster Rat empire.

Inui tells Saki that it was Kiroumaru who rescued him after he collapsed, but was subsequently taken prisoner. Saki receives a package and a letter from her mother in which she learns of an ancient weapon called the "Psychobuster", devised by normal humans to kill psychics. Saki and Satoru visit the imprisoned Kiroumaru, who offers them his help in finding the weapon's location, and the trio depart with Inui to the desert ruins of Tokyo to search for the Psychobuster. However, they fail to bypass the Monster Rats' blockades undetected and soon after arriving in the dangerous wasteland, they learn Yakomaru, his army, and the Ogre have followed them there.

As Saki's group continues to make their way through the treacherous tunnels of Tokyo, they came across an underground river hidden within the caves. They split into two groups: One group with Satoru and Kiroumaru to drive away their pursuers and the other group with Saki and Inui to retrieve the submarine so that can continue their mission through the river. While making their way to the Psychobuster, they were attacked by a giant ragworm. Inui sacrifices his life so that Saki can continue on with her mission. After retrieving the Psychobuster from an abandoned building, she takes off towards the sun at daybreak. As she runs past the dilapidated scene of Tokyo, she is finally able to recall her last conversation with Shun. With her lost memories restored, an image of Shun appears before her.

Kiroumaru finds Saki and informs her that Satoru is slightly injured while they were separated. Kiroumaru then decides that they should lure the Ogre and counterattack. Satoru and Saki wait in a tunnel as Kiroumaru leaves to lure the Ogre. As the Ogre enters the tunnel, Saki sets a mirror in front of her. She looks confused momentarily and then screams and tries to attack them. To protect Saki, Satoru ends up throwing the Psychobuster at the Ogre, but Saki incinerates the Psychobuster with fire before it can infect both the Ogre and Satoru, as she could not bear to lose her last remaining close friend. Failing to defeat the Ogre, Kiroumaru appears and quickly distracts the Ogre as they escape. They hide in a corner in the tunnels as they anticipate Yakomaru's next move. Yakomaru offers to negotiate with Saki's group but his true motive is to discover their position through their voices. The Ogre passes by them while hiding. Saki remembers what Shun said subconsciously, that the child may not be an Ogre. Saki then realizes that they had a way to defeat the Ogre all along.

Saki realizes that the Ogre was conditioned to suffer the death feedback from killing Monster Rats instead of humans. Kiroumaru then confronts the Ogre disguised as a human, resulting in the deaths of both, after asking Saki to promise that at least his colony will be spared from the humans' vengeful wrath. With the rebellion finally suppressed, Yakomaru, having renounced his title and once more addressing himself as Squealer, is tried and sentenced to "Eternal Hell", with his body suffering excruciating pain while being regenerated indefinitely. Satoru later reveals to Saki that upon analyzing the Monster Rats' DNA, he discovered that they were created by infusing mole rat DNA into ordinary humans to prevent them from being a threat to humans with telekinesis. Saki then pays a visit to Squealer and sure that he was already punished enough, gives him a merciful death. Ten years pass, and the now married Saki and Satoru expect their first child, both positive that by the time it grows up, the world will be a better place.

In 2008 the novel received the 29th Nihon SF Taisho Award.[16] The anime series has been critically acclaimed in the years since its airing, cited as one of the 21st century's top anime by fans and reviewers.[34][35]